Brunskill EW et al. (2008) Atlas of gene expression in the developing kidney at microanatomic resolution. Dev Cell 15: 781–791

A new atlas of gene expression during multiple stages of nephron formation in the developing mouse kidney has been mapped out, representing the first genomics-level analysis of organogenesis in a mammalian organ. Comparison of this atlas with gene expression patterns in mutant mice might help the understanding of abnormalities in kidney development.

Laser capture microdissection or fluorescence-activated cell sorting were used to isolate and purify discrete cell populations in kidneys from 15.5-day-old embryonic transgenic mice. Given that new nephrons form on the surface of the developing kidney and mature nephrons are located deep within the structure, samples taken from a single time point could be used to examine gene expression states in multiple stages of nephron formation.

Microarray profiling was used to identify probe sets specific for 15 embryonic compartments of the developing kidney, which represented multiple developmental stages of the nephron. Assessment of the differential expression of genes identified 7,629 probe sets, with adjacent compartments in the developing kidney showing high levels of correlative gene expression. Few compartments, however, exhibited highly restricted gene expression patterns, bar the proximal tubule and the ureteral smooth muscle. The quality of the microarray data was then confirmed by in silico comparison with previously determined gene expression patterns and by in situ hybridization.

These results indicate that kidney development follows an analog model in which levels of gene expression are important, rather than a digital model based on an on–off pattern of gene expression.